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Newsletter - May 2019

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MEETING REPORT


“Genomic Education and Training for Healthcare”; sponsored by the ‘Global Consortium for Genomic Education (GC4GE)’, The Genomic Medicine Foundation, UK (www.genomicmedicine.org ); Convener: Professor Dhavendra Kumar; CEO & Medical Director- The Genomic Medicine Foundation (UK).

This workshop was held on 24th April 2019, at the Human Genome Meeting 2019, Seoul, South Korea. Aims and objectives included-

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Consortium Update - March 2019

 

Plase find the link to our latest newsletter here:

https://mailchi.mp/275f0115a780/gc6jdli57c

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HGVS nomenclature course @ HGM2019

 

 
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                Seoul, South Korea - Wednesday 24 April 2019


 

Interested in HGVS nomenclature? Want to learn the basics? Want to increase your knowledge? Wiling to test your skills in describing variants?

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Consortium Update - July 2018
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GG2020 2018 Conference -
Precision Medicine in Thalassaemia

7th & 8th July 2018  Penang, Malaysia. 

GG2020 2020 Challenge has been making great progress in recent months. There are two important achievements to report.

First is the recent successful meeting of members held in Penang Malaysia in early July. This international meeting profiled what was happening in different parts of the world with several keynote presentations from key partners to the project, including Prof Sir John Burn, Dr Carsten Lederer from CING Cyprus and Dr Michael Angastiniotis CMO from TIF. Topics covered included addressing needs of patients in low resource settings, complexities of genotype and phenotype linking,  the challenge of incorporating precision medicine into haemoglobinopathies. The full program can be reviewed on the GG2020 website and the presenters slides are available – click here 
 
The team from Malaysia, led by Professor Zilfalil bin Alwi, who heads the Malaysian Country Node and it Co-chair of GG2020, are to be congratulated on organizing these quality meetings.
Delegates stayed on to participate in the annual meeting of the Malaysian Society of Human Genetics and the ASEAN Biomolecular Society meeting.
 
Second is to report that GG2020 Challenge has received funding for three years for a project to expand and ‘internationalise’ the ITHANET database and portal. This database forms the core of GG2020 activities and is based at CING in Cyprus. Following the establishment of an international expert panel to provide formal input to ClinGen on haemoglobinopathies as part of GG20202, it has become increasingly necessary to fund this work and expand the team who curates ITHANET.  Those wanting the know more about this should contact Petros Kountouris who is leading the project - petrosk@cing.ac.cy  - we thank the Cyprus Research Promotion Foundation who has provide the funding. Partners to the project are looking forward to three more years of successful work!


Blockchain – heard about it? Interested in it?  

In recent months, members of the Gene and Disease Locus Specific Database Council (GDLSC) of Global Variome have been sharing knowledge on this new technology and debating its utility for variant databases.  This is a call for anyone interested in following this topic and being linked up to a few others who are tracking developments. If you are interested in being part of the group to monitor blockchain technologies, discuss and occasionally report back to HVP members and Councils – please contact Helen Robinson – hmro@unimelb.edu.au

 

You may be aware that LOVD is undergoing some organizational changes to ensure its sustainability and will be moving under the auspices of the HVP (Human Variome Project).  As part of this, we are planning to form a user group aimed at involving LOVD users more directly in its development whilst providing more training and support for users.  The use of LOVD has once again grown rapidly in the past year with many more users, so it seems a good time to do this.

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HGVS nomenclature course @ ESHG 2018

 

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                Milan, Friday June 15, 2018

with the kind support of the European Society of Human Genetics

 

Background

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HVP @ Human Genome Meeting 2018, Yokohama

HVP will offer several important sessions at HuGO 2018 in Yokohama.  The speakers have been selected to profile what is currently happening in international variant information sharing, with emphasis on projects which are making great strides in resolving the practical issues in order to accelerate progress in all parts of the world. Different aspects have been highlighted including: the need for standardized approaches to describe and share variants; the practical case for sharing global knowledge - BRCA Exchange – is explained together with further local examples; the case for equitable use of genomics in clinical practice and the implications for ensuring knowledge of the context of diverse populations; how an approach to haemoglobinopathies can provide an example for promoting the use of genomic techniques in low and middle income countries for better health outcomes; and how the BRCA Exchange is helping to highlight the need for better quality genomic variant databases required for improved interpretation.

 

See program of HVP sessions below... 

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HGMprogramblog3

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Consortium Update - February 2018
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HVP Shared Database

 
Last year saw a considerable increase in the use of LOVD databases (numbers for Leiden/HVP hosted installations only):

  • The number of monthly page views increased from approximately 350,000 to almost 450,000 with the number of unique monthly visitors (each institute counted as one visitor) increased by 20,000.
  • The use of LOVD, api, computer requests for information increased from 4,000,000 to >39,000,000.

Statistics for the HVP shared gene variant database show a substantial increase as well:

  • The number of submitters, people actively sharing data with the HVP database, has grown in 2017 from 1046 to 1431.
  • The total number of variants in the database increased from 377,974 (49,238 unique) to 549,140 (79,224 unique), the number of individuals for which data were shared from 156,577 to 285,424

 
Total numbers (# installations, # individuals, # variants) for all public LOVD installations can be found on the LOVD website (http://www.lovd.nl/3.0/public_list)
 
Impressive numbers! We would like to thank all the LOVD team and it’s users for all their hard work.

 

 

        

 
A great start to 2018 as Dutch data now being shared with LOVD. Some time ago, the 9 Dutch clinical labs decided to share all classified variants which each other. They have now made an even bigger step and shared this data with the world. 

The project was initiated by the (Vereniging Klinisch Genetische Laboratoriumdiagnostiek, http://www.vkgl.nl), the Dutch association of laboratories for Clinical Genetics. Headed by Dr. Marielle van Gijn (UMC, Utrecht), the project first collected the data in a national repository built on Molgenis software, and checked whether variant classifications between labs agreed. 

The Dutch database currently contains over 90,000 classified variants. The variants for which there was consensus, roughly 28,000 classifications (>10,000 unique), have now been shared with the HVP shared database (LOVD). The variants can be found at https://databases.lovd.nl/shared, go to the Variants tab, select top option (View all genomic variants) and query for Owner "VKGL" (last column on the right). Soon all variants will be publically shared with both the HVP shared and ClinVar database.Our compliments and congratulations to the Dutch initiative. Which country is next?
    
 

ESHG, Milan 2018 - HGVS Nomenclature Course


Friday June 15, Milan (Italy)
Teach the Teacher:  HGVS nomenclature

 

A course on HGVS nomenclature, organised with financial support of the European Society of Human Genetics (ESHG), in collaboration with the Human Variome Project (HVP and the ESHG Education Committee.

HGVS nomenclature, currently supported by the HGVS, HVP, HUGO and GA4GH, is the language by which diagnostic reports as well as scientific reports on human genetic variation are drafted. Understanding this language and knowing how to use it is crucial for mutual understanding between geneticists and for the accuracy of diagnostic and scientific reporting in Human and Medical Genetics. A correct use of the HGVS recommendations prevents miscommunication and ensures that variants can be efficiently retrieved from existing data repositories facilitating variant annotation and classification.
The aim of the course is to give participants a detailed overview of the HGVS nomenclature. i.e. the recommendations for the description of sequence variants (Den Dunnen et al., 2017, Hum.Mutat. 37:564,;http://varnomen.HGVS.org). The course will have a “Teach the Teacher” format, i.e. after the course participants should be able to teach HGVS nomenclature to others. Registration to the course is free, but limited to 16-20 participants. Participants will be selected based on their willingness to act as a local (national) teacher and their expertise in the field. In addition we want to make sure participants are spread internationally, covering all continents on the globe. 

The entire course will be recorded (sound and video) and used to develop educational tools on HGVS nomenclature, including an e-learning module.

To register, please send a letter (max. A4) with your contact details and your motivation
ultimately April 15, 2018  to:

    ESHG Education Committee
        att. Johan den Dunnen

    VarNomen@HGVS.org

    Subject: HGVS course

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Message from the Executive Chairman - Dec 2017

Merry Christmas

 

Dear All

Firstly, I would like to take the opportunity to thank all HVP members for their contributions over the course of 2017. It has been a big year for us. As you know, it has been just over a year since I took over as Chair of the GV Board and during that time, there has been a lot of activity. We have seen open and transparent data sharing take off internationally, with substantially more interest in the core business of areas of HVP.

In particular, I would like to acknowledge the members of the various Councils of HVP – International Scientific Advisory Committee (ISAC), Gene/Disease Specific Database Advisory Council (G/DSDBAC) and International Confederation of Countries Advisory Council (ICCAC). Together with the Global Variome Board, these individuals make a valuable contribution to the work of HVP. Our achievements are the result of the work done by many of you who are based in research institutes, academic bodies, laboratories and the like. Linking up our activities and learning from each other underpins the progress of HVP.

 Discussions are continuing to align the LOVD databases, run by Johan den Dunnen, with the data centre under construction to support Genomics England. Johan has been very active leading our outreach and educational programmes. Activities this year have included the very successful academic meeting in Santiago de Compostela, a 3Gb training course in Mexico City and a well-supported Variant Interpretation training meeting in Prague. In 2018, we will seek to align our programme with the activities of the European Society of Human Genetics (ESHG) and organise another Variant Interpretation meeting in the East, possibly taking advantage of the Newcastle Medical Faculty facilities in southern Malaysia, adjacent to the Singapore border, offering excellent international travel links.

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